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2020-11-24gnu: tadbit: Update to 1.0.1....* gnu/packages/bioinformatics.scm (tadbit): Update to 1.0.1. [arguments]: Remove #:tests? and #:python arguments. [phases]{fix-problems-with-setup.py}: Remove no longer needed steps. {check}: Override phase. [native-inputs]: Add glib and pkg-config. [inputs]: Add python-future and python-h5py. Maxim Cournoyer
2020-11-24gnu: imp: Migrate to Python 3....* gnu/packages/bioinformatics.scm (imp) [arguments]: Enable tests by removing the #:tests? argument. Specify the arguments to pass to the ctest test running via the #:configure-flags argument. [inputs]: Add cgal and opencv. Remove python-2. Move swig to... [native-inputs]: ...here. Add python-wrapper. [propagated-inputs]: Replace python2-numpy, python2-scipy, python2-pandas, python2-scikit-learn and python2-networkx by python-numpy, python-scipy, python-pandas, python-scikit-learn and python-networkx, respectively. Maxim Cournoyer
2020-11-23gnu: Add cwltool....* gnu/packages/bioinformatics.scm (cwltool): New variable. Efraim Flashner
2020-11-23gnu: Add python-schema-salad....* gnu/packages/bioinformatics.scm (python-schema-salad): New variable. Efraim Flashner
2020-11-15gnu: methyldackel: Update to 0.5.1....* gnu/packages/bioinformatics.scm (methyldackel): Update to 0.5.1. [arguments]: Link with libbigwig. [inputs]: Add curl and libbigwig; replace htslib with htslib-1.9. Ricardo Wurmus
2020-11-13gnu: Fix build for python-pysam....* gnu/packages/bioinformatics.scm (python-pysam): Use htslib-1.9, samtools-1.9, and bcftools-1.9. Roel Janssen
2020-11-13gnu: Add bcftools-1.9....* gnu/packages/bioinformatics.scm (bcftools-1.9): New variable. Roel Janssen
2020-11-13gnu: bedtools: Use samtools-1.9....The build for bedtools with samtools 1.11 triggers a testsuite failure which is reported here: https://github.com/arq5x/bedtools2/issues/814 * gnu/packages/bioinformatics.scm (bedtools): Use samtools-1.9. Roel Janssen
2020-11-13gnu: Add samtools-1.9....* gnu/packages/bioinformatics.scm (samtools-1.9): New variable. Roel Janssen
2020-11-13gnu: Add htslib-1.9....* gnu/packages/bioinformatics.scm (htslib-1.9): New variable. Roel Janssen
2020-11-09gnu: macs: Remove generated code....* gnu/packages/bioinformatics.scm (macs)[source]: Add snippet to remove cython generated code. [native-inputs]: Add python-cython. Efraim Flashner
2020-11-09gnu: macs: Update check phase....* gnu/packages/bioinformatics.scm (macs)[arguments]: Don't delete 'check phase before using custom 'check phase. Efraim Flashner
2020-11-09gnu: macs: Update source, home-page URIs....* gnu/packages/bioinformatics.scm (macs)[source, home-page]: Update URIs to new location. Efraim Flashner
2020-10-29gnu: Update samtools to 1.11....* gnu/packages/bioinformatics.scm (samtools): Update to 1.11. Roel Janssen
2020-10-29gnu: Update bcftools to 1.11....* gnu/packages/bioinformatics.scm (bcftools): Update to 1.11. Roel Janssen
2020-10-29gnu: Update htslib to 1.11....* gnu/packages/bioinformatics.scm (htslib): Update to 1.11. Roel Janssen
2020-10-23gnu: imp: Update to 2.13.0....* gnu/packages/bioinformatics.scm (imp): Update to 2.13.0. Ludovic Courtès
2020-10-07gnu: htslib: Enable support for custom URI schemes....* gnu/packages/bioinformatics.scm (htslib)[arguments]: Enable support for custom URIs. Roel Janssen
2020-10-06gnu: r-gqtlbase: Update to 1.20.4....* gnu/packages/bioinformatics.scm (r-gqtlbase): Update to 1.20.4. Ricardo Wurmus
2020-10-06gnu: r-rhdf5: Update to 2.32.3....* gnu/packages/bioinformatics.scm (r-rhdf5): Update to 2.32.3. Ricardo Wurmus
2020-10-06gnu: r-biocstyle: Update to 2.16.1....* gnu/packages/bioinformatics.scm (r-biocstyle): Update to 2.16.1. Ricardo Wurmus
2020-09-25gnu: mafft: Update to 7.471....* gnu/packages/bioinformatics.scm (mafft): Update to 7.471. Signed-off-by: Mathieu Othacehe <othacehe@gnu.org> Mădălin Ionel Patrașcu
2020-09-22gnu: mafft: Use HTTPS home page URI....* gnu/packages/bioinformatics.scm (mafft)[home-page, license]: Use HTTPS URI. Nicolas Goaziou
2020-09-14gnu: r-fithic: Move to (gnu packages bioconductor)....* gnu/packages/bioinformatics.scm (r-fithic): Move from here... * gnu/packages/bioconductor.scm (r-fithic): ...to here. Signed-off-by: Ricardo Wurmus <rekado@elephly.net> zimoun
2020-09-14gnu: r-hitc: Move to (gnu packages bioconductor)....* gnu/packages/bioinformatics.scm (r-hitc): Move from here... * gnu/packages/bioconductor.scm (r-hitc): ...to here. Signed-off-by: Ricardo Wurmus <rekado@elephly.net> zimoun
2020-09-14gnu: r-hdf5array: Move to (gnu packages bioconductor)....* gnu/packages/bioinformatics.scm (r-hdf5array): Move from here... * gnu/packages/bioconductor.scm (r-hdf5array): ...to here. Signed-off-by: Ricardo Wurmus <rekado@elephly.net> zimoun
2020-09-14gnu: r-rhdf5lib: Move to (gnu packages bioconductor)....* gnu/packages/bioinformatics.scm (r-rhdf5lib): Move from here... * gnu/packages/bioconductor.scm (r-rhdf5lib): ...to here. Signed-off-by: Ricardo Wurmus <rekado@elephly.net> zimoun
2020-09-14gnu: r-beachmat: Move to (gnu packages bioconductor)....* gnu/packages/bioinformatics.scm (r-beachmat): Move from here... * gnu/packages/bioconductor.scm (r-beachmat): ...to here. Signed-off-by: Ricardo Wurmus <rekado@elephly.net> zimoun
2020-09-14gnu: r-singlecellexperiment: Move to (gnu packages bioconductor)....* gnu/packages/bioinformatics.scm (r-singlecellexperiment): Move from here... * gnu/packages/bioconductor.scm (r-singlecellexperiment): ...to here. Signed-off-by: Ricardo Wurmus <rekado@elephly.net> zimoun
2020-09-14gnu: r-scater: Move to (gnu packages bioconductor)....* gnu/packages/bioinformatics.scm (r-scater): Move from here... * gnu/packages/bioconductor.scm (r-scater): ...to here. Signed-off-by: Ricardo Wurmus <rekado@elephly.net> zimoun
2020-09-14gnu: r-scran: Move to (gnu packages bioconductor)....* gnu/packages/bioinformatics.scm (r-scran): Move from here... * gnu/packages/bioconductor.scm (r-scran): ...to here. Signed-off-by: Ricardo Wurmus <rekado@elephly.net> zimoun
2020-09-14gnu: r-delayedmatrixstats: Move to (gnu packages bioconductor)....* gnu/packages/bioinformatics.scm (r-delayedmatrixstats): Move from here... * gnu/packages/bioconductor.scm (r-delayedmatrixstats): ...to here. Signed-off-by: Ricardo Wurmus <rekado@elephly.net> zimoun
2020-09-11gnu: r-absfiltergsea: Move to (gnu packages cran)....* gnu/packages/bioinformatics.scm (r-absfiltergsea): Move from here... * gnu/packages/cran.scm (r-absfiltergsea): ...to here. Signed-off-by: Ricardo Wurmus <rekado@elephly.net> zimoun
2020-09-11gnu: r-diversitree: Move to (gnu packages cran)....* gnu/packages/bioinformatics.scm (r-diversitree): Move from here... * gnu/packages/cran.scm (r-diversitree): ...to here. Signed-off-by: Ricardo Wurmus <rekado@elephly.net> zimoun
2020-09-11gnu: r-phangorn: Move to (gnu packages cran)....* gnu/packages/bioinformatics.scm (r-phangorn): Move from here... * gnu/packages/cran.scm (r-phangorn): ...to here. Signed-off-by: Ricardo Wurmus <rekado@elephly.net> zimoun
2020-09-11gnu: r-seurat: Move to (gnu packages cran)....* gnu/packages/bioinformatics.scm (r-seurat): Move from here... * gnu/packages/cran.scm (r-seurat): ...to here. Signed-off-by: Ricardo Wurmus <rekado@elephly.net> zimoun
2020-09-11gnu: r-maldiquant: Move to (gnu packages cran)....* gnu/packages/bioinformatics.scm (r-maldiquant): Move from here... * gnu/packages/cran.scm (r-maldiquant): ...to here. Signed-off-by: Ricardo Wurmus <rekado@elephly.net> zimoun
2020-09-11gnu: r-seqminer: Move to (gnu packages cran)....* gnu/packages/bioinformatics.scm (r-seqminer): Move from here... * gnu/packages/cran.scm (r-seqminer): ...to here. Signed-off-by: Ricardo Wurmus <rekado@elephly.net> zimoun
2020-09-11gnu: r-qtl2: Move to (gnu packages cran)....* gnu/packages/bioinformatics.scm (r-qtl2): Move from here... * gnu/packages/cran.scm (r-qtl2): ...to here. Signed-off-by: Ricardo Wurmus <rekado@elephly.net> zimoun
2020-09-11gnu: r-qtl: Move to (gnu packages cran)....* gnu/packages/bioinformatics.scm (r-qtl): Move from here... * gnu/packages/cran.scm (r-qtl): ...to here. Signed-off-by: Ricardo Wurmus <rekado@elephly.net> zimoun
2020-09-10gnu: Move r-bisquerna....* gnu/packages/bioinformatics.scm (r-bisquerna): Move to ... * gnu/packages/cran.scm: ... here. Roel Janssen
2020-09-09Revert "gnu: Add r-loomr."...This reverts commit 1f56ec08af704bdc7aa3e143bf5ce351c5306dea. This package is not free software. Ricardo Wurmus
2020-09-09gnu: Add r-bisquerna....* gnu/packages/bioinformatics.scm (r-bisquerna): New variable. Roel Janssen
2020-09-09gnu: Add r-loomr....* gnu/packages/bioinformatics.scm (r-loomr): New variable. Roel Janssen
2020-09-05gnu: seqmagick: Update to 0.8.0....* gnu/packages/bioinformatics.scm (seqmagick): Update to 0.8.0. Andreas Enge
2020-08-30gnu: delly: Update to 0.8.3....* gnu/packages/bioinformatics.scm (delly): Update to 0.8.3. [inputs]: Order alphabetically. Efraim Flashner
2020-08-27gnu: vcflib: Install pkgconfig file....* gnu/packages/bioinformatics.scm (vcflib)[arguments]: Adjust custom 'install phase to add vcflib.pc. Efraim Flashner
2020-08-27gnu: vcflib: Use shared libraries....* gnu/packages/bioinformatics.scm (vcflib)[source]: Add patch. Add snippet to adjust files for new locations. [inputs]: Add fastahack, smithwaterman, tabixpp, xz. [native-inputs]: Add pkg-config. Remove the package-source of fastahack, fsom, smithwaterman, tabixpp. [arguments]: Remove make-flags. Add custom phase to add the output lib directory to the rpath. Adjust custom 'unpack-submodule-sources for the change in native-inputs. Adjust custom 'install phase to also install libraries and headers. * gnu/packages/patches/vcflib-use-shared-libraries.patch: New file. * gnu/local.mk (dist_patch_DATA): Register it. Efraim Flashner
2020-08-27gnu: fastahack: Install pkgconfig file....* gnu/packages/bioinformatics.scm (fastahack)[arguments]: Adjust custom 'install phase to add fastahack.pc. Efraim Flashner
2020-08-27gnu: fastahack: Build and install shared library and headers....* gnu/packages/bioinformatics.scm (fastahack)[arguments]: Add phase to build PIE objects. Add custom phase to build dynamic library. Adjust custom 'install phase to install shared library and headers. Efraim Flashner
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